6PGB

WDR5delta32 bound to N-(4-(5-(hydroxymethyl)-1H-imidazol-2-yl)butyl)-2-phenylacetamide


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2810.101 M ammonium sulfate, 0.1 M Bis-Tris chloride, pH 5.63, 25.8% w/v PEG4000
Crystal Properties
Matthews coefficientSolvent content
2.2144.39

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46.798α = 90
b = 65.275β = 90
c = 97.127γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2016-11-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAUSTRALIAN SYNCHROTRON BEAMLINE MX20.95370Australian SynchrotronMX2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)CC (Half)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.7348.5698.10.99612.613.631184
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.731.76800.8622.8

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 6PG41.7348.5629595153497.860.176120.1740.21697RANDOM10.552
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
-0.71-0.791.51
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.48
r_dihedral_angle_4_deg22.107
r_dihedral_angle_3_deg13.39
r_dihedral_angle_1_deg8.575
r_long_range_B_refined4.47
r_long_range_B_other4.469
r_angle_other_deg2.35
r_scangle_other1.578
r_angle_refined_deg1.407
r_mcangle_it1.331
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.48
r_dihedral_angle_4_deg22.107
r_dihedral_angle_3_deg13.39
r_dihedral_angle_1_deg8.575
r_long_range_B_refined4.47
r_long_range_B_other4.469
r_angle_other_deg2.35
r_scangle_other1.578
r_angle_refined_deg1.407
r_mcangle_it1.331
r_mcangle_other1.33
r_scbond_it0.974
r_scbond_other0.947
r_mcbond_it0.764
r_mcbond_other0.763
r_chiral_restr0.065
r_bond_other_d0.036
r_bond_refined_d0.009
r_gen_planes_other0.009
r_gen_planes_refined0.007
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2360
Nucleic Acid Atoms
Solvent Atoms352
Heterogen Atoms36

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing